chiMix_pDiff: Difference from nominal P-values of a chi-squared mixture.
In kjgleason/Primo: Package in R for Integrative Multi-Omics association analysis

Description Usage Arguments Details Value

Match observed P-values to nominal P-values by rank and calculate total difference. Objective function of a chi-squared mixture is used. This function is optimized to estimate the unknown scale and degree of freedom parameters for the scaled chi-squared distribution under the alternative hypothesis.

1	chiMix_pDiff(par, data, sorted = FALSE)

`par`	vector of two parameters for the alternative distribution: scale parameter [1] and degrees of freedom [2].
`data`	list with two elements: `chi_mix` (vector) and `alt_prop` (scalar).
`sorted`	logical, denoting whether `data$chi_mix` is sorted in decreasing order.

The argument data should be a two-element list. The first element, named chi_mix, is a vector of the observed values from the chi-squared mixture. The second element, named alt_prop, is the proportion of statistics that come from the alternative distribution.

The order of parameters is important in par. The scale parameter should be in the first position; the degrees of freedom should be in the second position.

A numeric value of the total (absolute) difference between observed P-values (given the parameters) and nominal P-values (given their ranks).

kjgleason/Primo documentation built on Sept. 7, 2021, 3:58 a.m.